An important clarification has been provided by the Central Board of Indirect Taxes and Customs (CBIC) regarding the imposition of late fees for the delay in submitting the reconciliation statement in Form GSTR-9C under the Goods and Services Tax (GST) framework through circular number 246.
From various representations, the same clarification arrives which urges clarity on whether the late fees shall be applicable when the GSTR-9C is submitted post-deadline, even when it is submitted after the due date for submitting the annual return in Form GSTR-9.
From the clarifications, the question is been addressed if the late fee u/s 47 of the Central Goods and Services Tax (CGST) Act, will be applicable if the GSTR-9C is filed after the deadline.
It is been mentioned by CBIC that a registered taxpayer is needed to submit the annual return (GSTR-9) including a reconciliation statement (GSTR-9C) if their aggregate turnover surpasses the specified threshold, which presently is at ₹5 crore.
A complete annual return forms both the GSTR-9 and the self-certified reconciliation statement in GSTR-9C, under GST provisions. The annual return filing is regarded as incomplete and a late fee is to be paid by the taxpayer if the reconciliation statement is not filed along with the GSTR-9.
A late fee is applicable for the delay in furnishing the complete annual return, which includes both form GSTR-9 and form GSTR-9C, as per Section 47(2) of the CGST Act. CBIC specified that the late fee shall not be computed separately for the late submission of GSTR-9 or GSTR-9C but instead for the whole late filing of the annual return.
In cases where there is no need for the reconciliation statement applies merely for the late submitting GSTR-9. For taxpayers who must submit both forms the late fee shall be applicable from the last date for submitting the complete annual return (both GSTR-9 and GSTR-9C) till the actual filing date.
The CBIC in a relief to the taxpayers must emphasize that via notification No. 08/2025-Central Tax, the late fee for late filing of the complete annual return for any financial year up to FY 2022-23 has been exempted. As long as the GSTR-9C is filed by March 31, 2025, the exemption is applicable.
The exemption comprises the late fee surpassing the amount liable to get filed u/s 47 as long as the GSTR-9C is provided before the mentioned due date. But no refund shall be issued for the late fees filed before, according to the GST circular.
